Three years ago, when the Bush administration announced that Jose Padilla would be tried in a civilian court after being held as an enemy combatant without charges, civil libertarians derided the move. It was a cynical attempt to end-run the Supreme Court before it could change administration policy, they said.

On Friday, the Obama administration made a similar decision in a similar case: it indicted Ali Saleh Kahlah al-Marri, an accused enemy combatant long in detention limbo in South Carolina, on charges of giving aid to Al Qaeda. The government also asked the Supreme Court to dismiss Mr. Marri’s challenge to his detention.

This time, civil libertarians generally hailed it as an affirmation of the new president’s core principles. “This administration has taken another step forward to restore the rule of law to our national security policies by ending a case of indefinite detention without charge,” said Senator Patrick J. Leahy, Democrat of Vermont.

But has it really?

Experts on the Marri case and the constitutional issues involved suggest that it is still too early to tell how the new administration will handle the abundance of civil liberties issues created by the Bush administration. For all the hopes of civil libertarians, President Obama has not wholeheartedly joined their ranks.

Mr. Obama campaigned against the Bush administration’s detention policies, and said in his Inaugural Address that “we reject as false the choice between our safety and our ideals,” but the new administration’s first moves have been mixed. Declarations of openness have seemed to conflict with decisions like the one this month that continued the Bush administration’s efforts to use the state secrets doctrine to shut down trials.

In Mr. Marri’s case, the administration supported his right to a trial, but also asked the Supreme Court to dismiss his effort to contest the government’s power to detain him — a fundamental point that civil liberties lawyers had yearned to fight.

Experts said that the administration was attempting a clever straddle: supporting Mr. Marri’s rights to a trial while avoiding a high-court confrontation not of its own choosing.

Orin S. Kerr, a law professor at George Washington University, noted that winning at the Supreme Court would affirm extraordinarily broad detention powers for a president — “a position they might not have wanted to take in the first place,” he said.

But losing would also put the government in a difficult spot, said Stewart Baker, a former Bush administration official in the Department of Homeland Security. The administration may be leery of broad detention power but might still want to use it in the most extreme cases. “Hanging on to the possibility of using this theory in a new and different emergency,” he said, “is the sort of thing that prudent government lawyers are inclined to do.”

In fact, said Matthew Waxman, an expert in the legal aspects of terrorism at Columbia University law school and a former Defense Department official with responsibility for detainee affairs, the other two branches of the government may be just as reluctant as the executive to deal with the uncomfortable issues raised by this case, and “would like this to go away.”

The two-page indictment, approved Thursday by a federal grand jury in Peoria, Ill., and unsealed Friday afternoon, accuses Mr. Marri of conspiring to provide material support and resources to Al Qaeda, as well as actually providing the support and resources. The indictment was brief, and disclosed nothing of the government’s case.

If Mr. Marri is found guilty of both counts, he faces a maximum of 30 years in prison.

“This indictment shows our resolve to protect the American people and prosecute alleged terrorists to the full extent of the law,” Attorney General Eric H. Holder Jr. said in a statement. “In this administration, we will hold accountable anyone who attempts to do harm to Americans, and we will do so in a manner consistent with our values.”

The government contends that Mr. Marri is a “sleeper agent” for Al Qaeda who had met with Osama bin Laden and pledged to do his bidding in the United States; Mr. Marri arrived in this country on Sept. 10, 2001.

Mr. Marri, who has been held without charges in the Navy brig in Charleston, S.C., for more than five years, has maintained his innocence, and his lawyers have challenged his detention.

In December, the Supreme Court agreed to hear the case, and scheduled oral arguments for April. President Obama ordered an interagency review of the Marri case in January, and received a memorandum on the matter on Thursday. On Friday, the president ordered the transfer of Mr. Marri’s case from the military to the Department of Justice.

The government’s request to dismiss the Supreme Court case suggested an alternative that that seemed to show its discomfort with the detention doctrine: it noted that the court might erase a 2007 appeals court decision that said Mr. Marri could be held by the military, and then instruct the lower court to dismiss the case.

Mr. Marri’s lead lawyer, Jonathan Hafetz of the American Civil Liberties Union, criticized that request, saying the question of the president’s power to detain people without charge needs to be resolved by the Supreme Court, “so it will not happen in the future,” he said.

Eric Posner, a professor of law at the University of Chicago, said that it is clear even now that the administration is going to act cautiously in these cases.

“They are going to put off as long as possible tying their hands in any way,” he said.

Such logic does not sit well with Eric Freedman, an expert in constitutional law at Hofstra University law school and a member of the Marri defense team. President Obama, he said, must decide whether he is “pursuing short-term flexibility at the cost of doing damage to the long-term rule of law.”